PONE-D-21-29146Single-cell Chromatin Accessibility and Lipid Profiling Reveals SCD1-dependent Metabolic Shift in Adipocytes After Bariatric SurgeryPLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In the manuscript entitled “Single-cell Chromatin Accessibility and Lipid Profiling Reveals SCD1-dependent Metabolic Shift in Adipocytes After Bariatric Surgery ”, Harlan and colleagues utilized single nucleus ATAC sequencing (snATAC) to study the mechanism of energy homeostasis and utilization in adipose tissue after bariatric surgery in mice. The authors showed the functional heterogeneity in the adipose tissues by unsupervised clustering analysis. They claimed that accessibility at some transcriptional factor motif (STAT5A, NFIC and NR1C3) changed in inguinal VSG adipocytes, therefore causing metabolism improvement and inflammation reduction. The profiling by snATAC and lipid profiling suggest reduced accumulation of unsaturated fatty acids produced by SCD1 could be the underlying mechanism of bariatric surgery’s beneficial effects.

Overall, this is an interesting work, which could be a reference for other studies. However, in order to serve as reliable reference, some additional validations of the bioinformatics data are needed. In addition, the sample size is relatively small, the authors may need to address the possibility of the genetic variations among the samples.

Some other concerns are listed below:

1. In the assay for the accessibility at transcription factor motifs, the authors combined all the classes of adipocytes. It might prevent the authors from finding out some subtype-specific transcriptional factors to address the heterogeneity of the mature adipocytes.

2. Validations for some of the key computational findings in the study will significantly increase the impact of this study. For one example, a chromatin-immunoprecipitation qPCR may help to validate identified interactions.  For another example, it will be more convincing if the authors validate the SCD1 changes by qPCR or western blotting.

3. Same amounts (80mg) of adipose tissue were used for analysis. However, there are more VSG cells passing the cutoff (Fig S1A). Does it mean more VSG cells were used for experiments and the cell volume of VSG adipose tissue are smaller than those in SHAM groups? Are there more TAG accumulation in the adipocytes of SHAM mice? If so, the transcriptional alternation could be the confounding effect of the TAG accumulation.

4. Some details are missing in the Methods part. Were the samples processed in the same time or in different batches? Was batch correction analysis performed? How were the samples selected for nuclei isolation after the adipose tissue minced? These details need to be provided to help understanding the results.

5.  “To classify cell types within these clusters, we used gene ontology (GO) enrichment for the top 200 differentially accessible genes from each cluster to provide insight into biological processes (fig 1c and fig S2c).” Eventually, Fig S2c lists top 500 DA genes. Please clarify. 

6. “We then confirmed the cell type assignment using known marker genes (Fig 2d, e).” It  should be Fig 1d,e

Reviewer #2: The manuscript by Harlan, et al. reported a single-cell chromatin accessibility analysis in the subcutaneous and epidydimal fat pads post the VSG surgery. To validate their findings, a further lipid profiling was performed. Authors identified fat depot-specific cell composition and chromatin accessibility, and their different response to the VSG surgery. In particular, the change in chromatin accessibility at Scd1 in the subcutaneous fat might explain the beneficial effects of the VSG surgery in mice. Overall, this is a well-designed and well-executed study. I only have a few minor suggestions.

1. The benefits in mice after the VSG mice need to be shown as supporting data, such as body weight, glucose tolerance, etc.

2. A main criticizing point is that authors failed to discuss the recent paper by Backhahl, et al. (Cell Metab 33, 1869-1882) describing distinct human adipocyte subpopulations and their differential sensitivities to insulin. How these subpopulations correlate to the three mature adipocyte subpopulations identified in the current study?

3. In this study, authors focused on the subcutaneous and epidydimal white adipose tissue. What is the change in the brown fat pad after the VSG surgery?

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Reviewer #1: No

Reviewer #2: No

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Single-cell  chromatin accessibility  and  lipid profiling reveals  SCD1-dependent  metabolic shift  in  adipocytes induced by bariatric surgery

PONE-D-21-29146R1

Dear Dr. Soloway,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kai Sun, MD, Ph.D

Associate Professor

Academic Editor

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In the revised manuscript, the authors addressed the questions and made the changes about the issues raised in the original review. I do think the revised manuscript well meets the publishable standard of the journal.

Reviewer #2: (No Response)

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If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No